Hey, jen.
1) Common question, if it makes you feel better. Common answer then: That's not how it works. When a DVD has a Director's commentary is not like that track is played back with the original soundrtrack in the background. You basically have to make two complete audio mixes. The original mix and a new full mix with the Director's commentary in it, with audio fades and all. THAT's what you use in track #2 (in this case, of course!)
2) There's no reason why it will play back with audio #2 unless the viewer chose that in the extra menu you made. If you force it to audio #1 in the track (which you of course you can), audio #2 will not work when the viewer wants it. One thing that may help, though - you could label audio track #2 as some bizarre language. Why? Because if it's labeled as English, Spanish, German or such a language, there is a chance that the viewers sets his DVD player to choose his prefered language. And if that language is the same as the label for audio #2, it will play that.
Hope this helps.
Adolfo Rozenfeld
Buenos Aires - Argentina
www.adolforozenfeld.com